6O7T

Saccharomyces cerevisiae V-ATPase Vph1-VO


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural comparison of the vacuolar and Golgi V-ATPases fromSaccharomyces cerevisiae.

Vasanthakumar, T.Bueler, S.A.Wu, D.Beilsten-Edmands, V.Robinson, C.V.Rubinstein, J.L.

(2019) Proc. Natl. Acad. Sci. U.S.A. 116: 7272-7277

  • DOI: 10.1073/pnas.1814818116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal acidification. In mammals, V-ATPase subunit isoforms are diffe ...

    Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal acidification. In mammals, V-ATPase subunit isoforms are differentially targeted to various intracellular compartments or tissues, but how these subunit isoforms influence enzyme activity is not clear. In the yeast Saccharomyces cerevisiae , isoform diversity is limited to two different versions of the proton-translocating subunit a: Vph1p, which is targeted to the vacuole, and Stv1p, which is targeted to the Golgi apparatus and endosomes. We show that purified V-ATPase complexes containing Vph1p have higher ATPase activity than complexes containing Stv1p and that the relative difference in activity depends on the presence of lipids. We also show that V O complexes containing Stv1p could be readily purified without attached V 1 regions. We used this effect to determine structures of the membrane-embedded V O region with Stv1p at 3.1-Å resolution, which we compare with a structure of the V O region with Vph1p that we determine to 3.2-Å resolution. These maps reveal differences in the surface charge near the cytoplasmic proton half-channel. Both maps also show the presence of bound lipids, as well as regularly spaced densities that may correspond to ergosterol or bound detergent, around the c-ring.


    Organizational Affiliation

    Physical and Theoretical Chemistry Laboratory, University of Oxford, OX1 3QZ Oxford, United Kingdom.,Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; john.rubinstein@utoronto.ca.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit a, vacuolar isoform
a
862Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VPH1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P32563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32563
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V0 assembly protein 1
b
265Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VOA1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P53262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53262
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c''
c
213Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA16 (PPA1)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P23968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23968
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit d
d
345Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA6
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32366
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Putative protein YPR170W-B
f
85Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P0C5R9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C5R9
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c
g, h, i, j, k, l, m, n
160Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA3 (CLS7, CUP5, GEF2)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25515
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c'
o
164Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA11 (CLS9, TFP3)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for P32842 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32842
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit e
e
73Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMA9 (CWH36, LDB10)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
Heterotrimeric EGChead Peripheral Stalk Complex
Find proteins for Q3E7B6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E7B6
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaMOP81294

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-10
    Type: Data collection, Database references
  • Version 1.2: 2019-04-24
    Type: Data collection, Database references